2 |
|
#include "simError.h" |
3 |
|
#include <cmath> |
4 |
|
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
5 |
< |
: T(theInfo, the_ff), fz(NULL), |
6 |
< |
indexOfZConsMols(NULL) |
5 |
> |
: T(theInfo, the_ff), fz(NULL), curZPos(NULL), |
6 |
> |
indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0) |
7 |
|
{ |
8 |
|
|
9 |
|
//get properties from SimInfo |
11 |
|
ZConsParaData* zConsParaData; |
12 |
|
DoubleData* sampleTime; |
13 |
|
DoubleData* tolerance; |
14 |
+ |
StringData* policy; |
15 |
|
StringData* filename; |
16 |
|
double COM[3]; |
17 |
|
|
27 |
|
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
28 |
|
zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
29 |
|
|
30 |
+ |
//creat force substraction policy |
31 |
+ |
data = info->getProperty(ZCONSFORCEPOLICY_ID); |
32 |
+ |
if(!data){ |
33 |
+ |
sprintf( painCave.errMsg, |
34 |
+ |
"ZConstraint Warning: User does not set force substraction policy, " |
35 |
+ |
"PolicyByMass is used\n"); |
36 |
+ |
painCave.isFatal = 0; |
37 |
+ |
simError(); |
38 |
+ |
|
39 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
40 |
+ |
} |
41 |
+ |
else{ |
42 |
+ |
policy = dynamic_cast<StringData*>(data); |
43 |
+ |
|
44 |
+ |
if(!policy){ |
45 |
+ |
sprintf( painCave.errMsg, |
46 |
+ |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
47 |
+ |
"PolicyByMass is used\n"); |
48 |
+ |
painCave.isFatal = 0; |
49 |
+ |
simError(); |
50 |
+ |
|
51 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
52 |
+ |
} |
53 |
+ |
else{ |
54 |
+ |
if(policy->getData() == "BYNUMBER") |
55 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
56 |
+ |
else if(policy->getData() == "BYMASS") |
57 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
58 |
+ |
else{ |
59 |
+ |
sprintf( painCave.errMsg, |
60 |
+ |
"ZConstraint Warning: unknown force substraction policy, " |
61 |
+ |
"PolicyByMass is used\n"); |
62 |
+ |
painCave.isFatal = 0; |
63 |
+ |
simError(); |
64 |
+ |
forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
65 |
+ |
} |
66 |
+ |
} |
67 |
+ |
} |
68 |
+ |
|
69 |
+ |
|
70 |
|
//retrieve sample time of z-contraint |
71 |
|
data = info->getProperty(ZCONSTIME_ID); |
72 |
|
|
110 |
|
} |
111 |
|
else{ |
112 |
|
|
113 |
< |
filename = dynamic_cast<StringData*>(data); |
113 |
> |
filename = dynamic_cast<StringData*>(data); |
114 |
|
|
115 |
|
if(!filename){ |
116 |
|
|
124 |
|
this->zconsOutput = filename->getData(); |
125 |
|
} |
126 |
|
|
86 |
– |
|
127 |
|
} |
128 |
|
|
129 |
|
//retrieve tolerance for z-constraint molecuels |
153 |
|
} |
154 |
|
|
155 |
|
} |
156 |
< |
|
156 |
> |
|
157 |
|
//retrieve index of z-constraint molecules |
158 |
|
data = info->getProperty(ZCONSPARADATA_ID); |
159 |
|
if(!data) { |
194 |
|
"ZConstraint error: index is out of range\n"); |
195 |
|
painCave.isFatal = 1; |
196 |
|
simError(); |
197 |
< |
} |
197 |
> |
} |
198 |
|
|
199 |
< |
maxIndex = (*parameters)[parameters->size()].zconsIndex; |
199 |
> |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
200 |
|
|
201 |
|
#ifndef IS_MPI |
202 |
|
totalNumMol = nMols; |
215 |
|
//its initial z coordinate will be used as default |
216 |
|
for(int i = 0; i < parameters->size(); i++){ |
217 |
|
|
218 |
< |
if(!(*parameters)[i].havingZPos){ |
179 |
< |
|
218 |
> |
if(!(*parameters)[i].havingZPos){ |
219 |
|
#ifndef IS_MPI |
220 |
< |
for(int j = 0; j < nMols; j++){ |
221 |
< |
if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
222 |
< |
molecules[i].getCOM(COM); |
223 |
< |
break; |
185 |
< |
} |
220 |
> |
for(int j = 0; j < nMols; j++){ |
221 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
222 |
> |
molecules[j].getCOM(COM); |
223 |
> |
break; |
224 |
|
} |
225 |
+ |
} |
226 |
|
#else |
227 |
|
//query which processor current zconstraint molecule belongs to |
228 |
< |
int *MolToProcMap; |
229 |
< |
int whichNode; |
230 |
< |
double initZPos; |
231 |
< |
MolToProcMap = mpiSim->getMolToProcMap(); |
232 |
< |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
233 |
< |
|
234 |
< |
//broadcast the zpos of current z-contraint molecule |
235 |
< |
//the node which contain this |
228 |
> |
int *MolToProcMap; |
229 |
> |
int whichNode; |
230 |
> |
double initZPos; |
231 |
> |
MolToProcMap = mpiSim->getMolToProcMap(); |
232 |
> |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
233 |
> |
|
234 |
> |
//broadcast the zpos of current z-contraint molecule |
235 |
> |
//the node which contain this |
236 |
|
|
237 |
< |
if (worldRank == whichNode ){ |
238 |
< |
|
239 |
< |
for(int i = 0; i < nMols; i++) |
240 |
< |
if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
241 |
< |
molecules[i].getCOM(COM); |
242 |
< |
break; |
243 |
< |
} |
244 |
< |
|
245 |
< |
} |
237 |
> |
if (worldRank == whichNode ){ |
238 |
> |
|
239 |
> |
for(int j = 0; j < nMols; j++) |
240 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
241 |
> |
molecules[j].getCOM(COM); |
242 |
> |
break; |
243 |
> |
} |
244 |
> |
|
245 |
> |
} |
246 |
|
|
247 |
< |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
247 |
> |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
248 |
|
#endif |
249 |
|
|
250 |
< |
(*parameters)[i].zPos = COM[whichDirection]; |
250 |
> |
(*parameters)[i].zPos = COM[whichDirection]; |
251 |
|
|
252 |
< |
sprintf( painCave.errMsg, |
253 |
< |
"ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
252 |
> |
sprintf( painCave.errMsg, |
253 |
> |
"ZConstraint warning: Does not specify zpos for z-constraint molecule " |
254 |
|
"initial z coornidate will be used \n"); |
255 |
< |
painCave.isFatal = 0; |
256 |
< |
simError(); |
257 |
< |
|
258 |
< |
} |
259 |
< |
} |
260 |
< |
|
255 |
> |
painCave.isFatal = 0; |
256 |
> |
simError(); |
257 |
> |
|
258 |
> |
} |
259 |
> |
} |
260 |
> |
|
261 |
|
}//end if (!zConsParaData) |
262 |
|
}//end if (!data) |
263 |
|
|
277 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
278 |
|
|
279 |
|
zPos.push_back((*parameters)[searchResult].zPos); |
280 |
< |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
280 |
> |
// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
281 |
> |
// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
282 |
> |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
283 |
|
|
284 |
|
molecules[i].getCOM(COM); |
285 |
|
} |
293 |
|
} |
294 |
|
|
295 |
|
fz = new double[zconsMols.size()]; |
296 |
+ |
curZPos = new double[zconsMols.size()]; |
297 |
|
indexOfZConsMols = new int [zconsMols.size()]; |
298 |
|
|
299 |
< |
if(!fz || !indexOfZConsMols){ |
299 |
> |
if(!fz || !curZPos || !indexOfZConsMols){ |
300 |
|
sprintf( painCave.errMsg, |
301 |
|
"Memory allocation failure in class Zconstraint\n"); |
302 |
|
painCave.isFatal = 1; |
303 |
|
simError(); |
304 |
|
} |
305 |
|
|
306 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
306 |
> |
//determine the states of z-constraint molecules |
307 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
308 |
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
309 |
+ |
|
310 |
+ |
zconsMols[i]->getCOM(COM); |
311 |
+ |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
312 |
+ |
states.push_back(zcsFixed); |
313 |
+ |
else |
314 |
+ |
states.push_back(zcsMoving); |
315 |
+ |
} |
316 |
|
|
317 |
|
#endif |
318 |
|
|
319 |
+ |
//get total masss of unconstraint molecules |
320 |
+ |
double totalMassOfUncons_local; |
321 |
+ |
totalMassOfUncons_local = 0; |
322 |
+ |
|
323 |
+ |
for(int i = 0; i < unconsMols.size(); i++) |
324 |
+ |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
325 |
+ |
|
326 |
+ |
#ifndef IS_MPI |
327 |
+ |
totalMassOfUncons = totalMassOfUncons_local; |
328 |
+ |
#else |
329 |
+ |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
330 |
+ |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
331 |
+ |
#endif |
332 |
+ |
|
333 |
+ |
|
334 |
|
//get total number of unconstrained atoms |
335 |
|
int nUnconsAtoms_local; |
336 |
|
nUnconsAtoms_local = 0; |
340 |
|
#ifndef IS_MPI |
341 |
|
totNumOfUnconsAtoms = nUnconsAtoms_local; |
342 |
|
#else |
343 |
< |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
344 |
< |
#endif |
343 |
> |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
344 |
> |
MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
345 |
> |
#endif |
346 |
|
|
347 |
< |
checkZConsState(); |
348 |
< |
|
283 |
< |
// |
284 |
< |
fzOut = new ZConsWriter(zconsOutput.c_str()); |
347 |
> |
// creat zconsWriter |
348 |
> |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
349 |
|
|
350 |
|
if(!fzOut){ |
351 |
|
sprintf( painCave.errMsg, |
353 |
|
painCave.isFatal = 1; |
354 |
|
simError(); |
355 |
|
} |
356 |
< |
|
356 |
> |
|
357 |
> |
forcePolicy->update(); |
358 |
|
} |
359 |
|
|
360 |
|
template<typename T> ZConstraint<T>::~ZConstraint() |
361 |
|
{ |
362 |
|
if(fz) |
363 |
|
delete[] fz; |
364 |
+ |
|
365 |
+ |
if(curZPos) |
366 |
+ |
delete[] curZPos; |
367 |
|
|
368 |
|
if(indexOfZConsMols) |
369 |
|
delete[] indexOfZConsMols; |
370 |
|
|
371 |
|
if(fzOut) |
372 |
|
delete fzOut; |
373 |
+ |
|
374 |
+ |
if(forcePolicy) |
375 |
+ |
delete forcePolicy; |
376 |
|
} |
377 |
|
|
378 |
+ |
|
379 |
+ |
/** |
380 |
+ |
* |
381 |
+ |
*/ |
382 |
+ |
|
383 |
|
#ifdef IS_MPI |
384 |
|
template<typename T> void ZConstraint<T>::update() |
385 |
|
{ |
404 |
|
|
405 |
|
zconsMols.push_back(&molecules[i]); |
406 |
|
zPos.push_back((*parameters)[index].zPos); |
407 |
< |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
408 |
< |
|
407 |
> |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
408 |
> |
|
409 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
410 |
|
|
411 |
|
molecules[i].getCOM(COM); |
418 |
|
|
419 |
|
} |
420 |
|
} |
421 |
+ |
|
422 |
+ |
//determine the states of z-constraint molecules |
423 |
+ |
for(int i = 0; i < zconsMols.size(); i++){ |
424 |
+ |
zconsMols[i]->getCOM(COM); |
425 |
+ |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
426 |
+ |
states.push_back(zcsFixed); |
427 |
+ |
else |
428 |
+ |
states.push_back(zcsMoving); |
429 |
+ |
} |
430 |
+ |
|
431 |
|
|
432 |
|
//The reason to declare fz and indexOfZconsMols as pointer to array is |
433 |
|
// that we want to make the MPI communication simple |
434 |
|
if(fz) |
435 |
|
delete[] fz; |
436 |
+ |
|
437 |
+ |
if(curZPos) |
438 |
+ |
delete[] curZPos; |
439 |
|
|
440 |
|
if(indexOfZConsMols) |
441 |
|
delete[] indexOfZConsMols; |
442 |
|
|
443 |
|
if (zconsMols.size() > 0){ |
444 |
|
fz = new double[zconsMols.size()]; |
445 |
+ |
curZPos = new double[zconsMols.size()]; |
446 |
|
indexOfZConsMols = new int[zconsMols.size()]; |
447 |
|
|
448 |
< |
if(!fz || !indexOfZConsMols){ |
448 |
> |
if(!fz || !curZPos || !indexOfZConsMols){ |
449 |
|
sprintf( painCave.errMsg, |
450 |
|
"Memory allocation failure in class Zconstraint\n"); |
451 |
|
painCave.isFatal = 1; |
459 |
|
} |
460 |
|
else{ |
461 |
|
fz = NULL; |
462 |
+ |
curZPos = NULL; |
463 |
|
indexOfZConsMols = NULL; |
464 |
|
} |
465 |
|
|
466 |
+ |
// |
467 |
+ |
forcePolicy->update(); |
468 |
+ |
|
469 |
|
} |
470 |
|
|
471 |
|
#endif |
472 |
|
|
473 |
< |
/** Function Name: isZConstraintMol |
474 |
< |
** Parameter |
475 |
< |
** Molecule* mol |
476 |
< |
** Return value: |
477 |
< |
** -1, if the molecule is not z-constraint molecule, |
478 |
< |
** other non-negative values, its index in indexOfAllZConsMols vector |
473 |
> |
/** |
474 |
> |
* Function Name: isZConstraintMol |
475 |
> |
* Parameter |
476 |
> |
* Molecule* mol |
477 |
> |
* Return value: |
478 |
> |
* -1, if the molecule is not z-constraint molecule, |
479 |
> |
* other non-negative values, its index in indexOfAllZConsMols vector |
480 |
|
*/ |
481 |
|
|
482 |
|
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
505 |
|
return -1; |
506 |
|
} |
507 |
|
|
413 |
– |
/** |
414 |
– |
* Description: |
415 |
– |
* Reset the z coordinates |
416 |
– |
*/ |
508 |
|
template<typename T> void ZConstraint<T>::integrate(){ |
509 |
|
|
510 |
|
//zero out the velocities of center of mass of unconstrained molecules |
511 |
|
//and the velocities of center of mass of every single z-constrained molecueles |
512 |
|
zeroOutVel(); |
513 |
+ |
|
514 |
+ |
curZconsTime = zconsTime + info->getTime(); |
515 |
|
|
516 |
|
T::integrate(); |
517 |
|
|
523 |
|
* |
524 |
|
* |
525 |
|
* |
526 |
< |
*/ |
434 |
< |
|
435 |
< |
|
526 |
> |
*/ |
527 |
|
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
528 |
+ |
double zsys; |
529 |
+ |
double COM[3]; |
530 |
+ |
double force[3]; |
531 |
+ |
double zSysCOMVel; |
532 |
|
|
533 |
|
T::calcForce(calcPot, calcStress); |
534 |
|
|
535 |
< |
if (checkZConsState()) |
535 |
> |
if (checkZConsState()){ |
536 |
> |
|
537 |
> |
#ifdef IS_MPI |
538 |
> |
if(worldRank == 0){ |
539 |
> |
#endif |
540 |
> |
// std::cerr << "\n" |
541 |
> |
// << "*******************************************\n" |
542 |
> |
// << " about to call zeroOutVel()\n" |
543 |
> |
// << "*******************************************\n" |
544 |
> |
// << "\n"; |
545 |
> |
#ifdef IS_MPI |
546 |
> |
} |
547 |
> |
#endif |
548 |
|
zeroOutVel(); |
549 |
|
|
550 |
+ |
#ifdef IS_MPI |
551 |
+ |
if(worldRank == 0){ |
552 |
+ |
#endif |
553 |
+ |
// std::cerr << "\n" |
554 |
+ |
// << "*******************************************\n" |
555 |
+ |
// << " finished zeroOutVel()\n" |
556 |
+ |
// << "*******************************************\n" |
557 |
+ |
// << "\n"; |
558 |
+ |
#ifdef IS_MPI |
559 |
+ |
} |
560 |
+ |
#endif |
561 |
+ |
|
562 |
+ |
forcePolicy->update(); |
563 |
+ |
} |
564 |
+ |
|
565 |
+ |
zsys = calcZSys(); |
566 |
+ |
zSysCOMVel = calcSysCOMVel(); |
567 |
+ |
#ifdef IS_MPI |
568 |
+ |
if(worldRank == 0){ |
569 |
+ |
#endif |
570 |
+ |
// cout << "---------------------------------------------------------------------" <<endl; |
571 |
+ |
// cout << "current time: " << info->getTime() << endl; |
572 |
+ |
// cout << "center of mass at z: " << zsys << endl; |
573 |
+ |
// cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
574 |
+ |
|
575 |
+ |
#ifdef IS_MPI |
576 |
+ |
} |
577 |
+ |
#endif |
578 |
+ |
|
579 |
|
//do zconstraint force; |
580 |
|
if (haveFixedZMols()) |
581 |
|
this->doZconstraintForce(); |
582 |
< |
|
582 |
> |
|
583 |
|
//use harmonical poteintial to move the molecules to the specified positions |
584 |
|
if (haveMovingZMols()) |
585 |
< |
//this->doHarmonic(); |
586 |
< |
|
587 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
588 |
< |
|
585 |
> |
this->doHarmonic(); |
586 |
> |
|
587 |
> |
//write out forces and current positions of z-constraint molecules |
588 |
> |
if(info->getTime() >= curZconsTime){ |
589 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
590 |
> |
zconsMols[i]->getCOM(COM); |
591 |
> |
curZPos[i] = COM[whichDirection]; |
592 |
> |
|
593 |
> |
//if the z-constraint molecule is still moving, just record its force |
594 |
> |
if(states[i] == zcsMoving){ |
595 |
> |
fz[i] = 0; |
596 |
> |
Atom** movingZAtoms; |
597 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
598 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
599 |
> |
movingZAtoms[j]->getFrc(force); |
600 |
> |
fz[i] += force[whichDirection]; |
601 |
> |
} |
602 |
> |
} |
603 |
> |
} |
604 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
605 |
> |
curZconsTime += zconsTime; |
606 |
> |
} |
607 |
> |
|
608 |
> |
zSysCOMVel = calcSysCOMVel(); |
609 |
> |
#ifdef IS_MPI |
610 |
> |
if(worldRank == 0){ |
611 |
> |
#endif |
612 |
> |
// cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
613 |
> |
#ifdef IS_MPI |
614 |
> |
} |
615 |
> |
#endif |
616 |
|
} |
617 |
+ |
|
618 |
+ |
|
619 |
+ |
/** |
620 |
+ |
* |
621 |
+ |
*/ |
622 |
|
|
623 |
|
template<typename T> double ZConstraint<T>::calcZSys() |
624 |
|
{ |
627 |
|
double totalMass; |
628 |
|
double totalMZ_local; |
629 |
|
double totalMZ; |
462 |
– |
double massOfUncons_local; |
630 |
|
double massOfCurMol; |
631 |
|
double COM[3]; |
632 |
|
|
633 |
|
totalMass_local = 0; |
467 |
– |
totalMass = 0; |
634 |
|
totalMZ_local = 0; |
469 |
– |
totalMZ = 0; |
470 |
– |
massOfUncons_local = 0; |
471 |
– |
|
635 |
|
|
636 |
|
for(int i = 0; i < nMols; i++){ |
637 |
|
massOfCurMol = molecules[i].getTotalMass(); |
639 |
|
|
640 |
|
totalMass_local += massOfCurMol; |
641 |
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
642 |
< |
|
480 |
< |
if(isZConstraintMol(&molecules[i]) == -1){ |
481 |
< |
|
482 |
< |
massOfUncons_local += massOfCurMol; |
483 |
< |
} |
484 |
< |
|
642 |
> |
|
643 |
|
} |
644 |
+ |
|
645 |
|
|
487 |
– |
|
646 |
|
#ifdef IS_MPI |
647 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
648 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
649 |
< |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
650 |
< |
#else |
647 |
> |
MPI_Allreduce(&totalMass_local, &totalMass, 1, |
648 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
649 |
> |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
650 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
651 |
> |
#else |
652 |
|
totalMass = totalMass_local; |
653 |
|
totalMZ = totalMZ_local; |
654 |
< |
totalMassOfUncons = massOfUncons_local; |
496 |
< |
#endif |
654 |
> |
#endif |
655 |
|
|
656 |
|
double zsys; |
657 |
|
zsys = totalMZ / totalMass; |
670 |
|
|
671 |
|
/** |
672 |
|
* |
515 |
– |
* |
516 |
– |
* |
673 |
|
*/ |
674 |
|
|
675 |
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
677 |
|
Atom** fixedZAtoms; |
678 |
|
double COMvel[3]; |
679 |
|
double vel[3]; |
680 |
< |
|
680 |
> |
double zSysCOMVel; |
681 |
> |
|
682 |
|
//zero out the velocities of center of mass of fixed z-constrained molecules |
683 |
|
|
684 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
685 |
|
|
686 |
< |
if (states[i] == zcsFixed){ |
686 |
> |
if (states[i] == zcsFixed){ |
687 |
|
|
688 |
< |
zconsMols[i]->getCOMvel(COMvel); |
688 |
> |
zconsMols[i]->getCOMvel(COMvel); |
689 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
690 |
> |
|
691 |
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
692 |
< |
|
692 |
> |
|
693 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
694 |
|
fixedZAtoms[j]->getVel(vel); |
695 |
< |
vel[whichDirection] -= COMvel[whichDirection]; |
696 |
< |
fixedZAtoms[j]->setVel(vel); |
695 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
696 |
> |
fixedZAtoms[j]->setVel(vel); |
697 |
|
} |
698 |
< |
|
698 |
> |
|
699 |
> |
zconsMols[i]->getCOMvel(COMvel); |
700 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
701 |
|
} |
541 |
– |
|
542 |
– |
} |
702 |
|
|
703 |
+ |
} |
704 |
+ |
|
705 |
+ |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
706 |
+ |
|
707 |
+ |
zSysCOMVel = calcSysCOMVel(); |
708 |
+ |
#ifdef IS_MPI |
709 |
+ |
if(worldRank == 0){ |
710 |
+ |
#endif |
711 |
+ |
// cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
712 |
+ |
#ifdef IS_MPI |
713 |
+ |
} |
714 |
+ |
#endif |
715 |
+ |
|
716 |
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
717 |
|
double MVzOfMovingMols_local; |
718 |
|
double MVzOfMovingMols; |
727 |
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
728 |
|
} |
729 |
|
|
730 |
< |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
559 |
< |
|
730 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
731 |
|
if (states[i] == zcsMoving){ |
732 |
|
zconsMols[i]->getCOMvel(COMvel); |
733 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
734 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
734 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
735 |
|
} |
736 |
< |
|
736 |
> |
|
737 |
|
} |
738 |
|
|
739 |
|
#ifndef IS_MPI |
762 |
|
|
763 |
|
//modify the velocities of moving z-constrained molecuels |
764 |
|
Atom** movingZAtoms; |
765 |
< |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
765 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
766 |
|
|
767 |
|
if (states[i] ==zcsMoving){ |
768 |
|
|
769 |
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
770 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
770 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
771 |
|
movingZAtoms[j]->getVel(vel); |
772 |
|
vel[whichDirection] -= vzOfMovingMols; |
773 |
< |
movingZAtoms[j]->setVel(vel); |
603 |
< |
} |
604 |
< |
|
773 |
> |
movingZAtoms[j]->setVel(vel); |
774 |
|
} |
775 |
+ |
|
776 |
+ |
} |
777 |
|
|
778 |
+ |
} |
779 |
+ |
|
780 |
+ |
|
781 |
+ |
zSysCOMVel = calcSysCOMVel(); |
782 |
+ |
#ifdef IS_MPI |
783 |
+ |
if(worldRank == 0){ |
784 |
+ |
#endif |
785 |
+ |
// cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
786 |
+ |
#ifdef IS_MPI |
787 |
|
} |
788 |
+ |
#endif |
789 |
|
|
790 |
|
} |
791 |
|
|
792 |
+ |
/** |
793 |
+ |
* |
794 |
+ |
*/ |
795 |
+ |
|
796 |
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
797 |
|
|
798 |
|
Atom** zconsAtoms; |
801 |
|
double COMvel[3]; |
802 |
|
double COM[3]; |
803 |
|
double force[3]; |
619 |
– |
double zsys; |
804 |
|
|
805 |
< |
int nMovingZMols_local; |
622 |
< |
int nMovingZMols; |
623 |
< |
|
624 |
< |
//constrain the molecules which do not reach the specified positions |
625 |
< |
|
626 |
< |
zsys = calcZSys(); |
627 |
< |
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
805 |
> |
//constrain the molecules which do not reach the specified positions |
806 |
|
|
807 |
|
//Zero Out the force of z-contrained molecules |
808 |
|
totalFZ_local = 0; |
809 |
|
|
810 |
|
//calculate the total z-contrained force of fixed z-contrained molecules |
811 |
< |
cout << "Fixed Molecules" << endl; |
811 |
> |
|
812 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
813 |
< |
|
813 |
> |
|
814 |
|
if (states[i] == zcsFixed){ |
815 |
< |
|
815 |
> |
|
816 |
|
zconsMols[i]->getCOM(COM); |
817 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
818 |
|
|
820 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
821 |
|
zconsAtoms[j]->getFrc(force); |
822 |
|
fz[i] += force[whichDirection]; |
823 |
< |
} |
823 |
> |
} |
824 |
|
totalFZ_local += fz[i]; |
825 |
|
|
826 |
< |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
826 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
827 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
828 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
829 |
|
|
830 |
+ |
|
831 |
|
} |
832 |
< |
|
832 |
> |
|
833 |
|
} |
834 |
|
|
835 |
< |
//calculate the number of atoms of moving z-constrained molecules |
655 |
< |
nMovingZMols_local = 0; |
656 |
< |
for(int i = 0; zconsMols.size(); i++){ |
657 |
< |
if(states[i] == zcsMoving) |
658 |
< |
nMovingZMols_local += massOfZConsMols[i]; |
659 |
< |
} |
835 |
> |
//calculate total z-constraint force |
836 |
|
#ifdef IS_MPI |
837 |
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
662 |
– |
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
838 |
|
#else |
839 |
|
totalFZ = totalFZ_local; |
665 |
– |
nMovingZMols = nMovingZMols_local; |
840 |
|
#endif |
841 |
|
|
842 |
+ |
|
843 |
+ |
// apply negative to fixed z-constrained molecues; |
844 |
|
force[0]= 0; |
845 |
|
force[1]= 0; |
846 |
|
force[2]= 0; |
671 |
– |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
847 |
|
|
848 |
< |
//modify the velocites of unconstrained molecules |
848 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
849 |
> |
|
850 |
> |
if (states[i] == zcsFixed){ |
851 |
> |
|
852 |
> |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
853 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
854 |
> |
|
855 |
> |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
856 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
857 |
> |
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
858 |
> |
zconsAtoms[j]->addFrc(force); |
859 |
> |
} |
860 |
> |
|
861 |
> |
} |
862 |
> |
|
863 |
> |
} |
864 |
> |
|
865 |
> |
// cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
866 |
> |
// << "total force is " << calcTotalForce() << endl; |
867 |
> |
|
868 |
> |
force[0]= 0; |
869 |
> |
force[1]= 0; |
870 |
> |
force[2]= 0; |
871 |
> |
|
872 |
> |
//modify the forces of unconstrained molecules |
873 |
|
for(int i = 0; i < unconsMols.size(); i++){ |
874 |
|
|
875 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
876 |
|
|
877 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
877 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
878 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
879 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
880 |
|
unconsAtoms[j]->addFrc(force); |
881 |
+ |
} |
882 |
|
|
883 |
|
} |
884 |
|
|
885 |
< |
//modify the velocities of moving z-constrained molecules |
885 |
> |
//modify the forces of moving z-constrained molecules |
886 |
|
for(int i = 0; i < zconsMols.size(); i++) { |
887 |
< |
if (states[i] == zcsMoving){ |
888 |
< |
|
889 |
< |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
887 |
> |
if (states[i] == zcsMoving){ |
888 |
> |
|
889 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
890 |
|
|
891 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
892 |
< |
movingZAtoms[j]->addFrc(force); |
893 |
< |
} |
891 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
892 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
893 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
894 |
> |
movingZAtoms[j]->addFrc(force); |
895 |
> |
} |
896 |
> |
} |
897 |
|
} |
898 |
|
|
899 |
< |
// apply negative to fixed z-constrained molecues; |
900 |
< |
force[0]= 0; |
696 |
< |
force[1]= 0; |
697 |
< |
force[2]= 0; |
899 |
> |
//cout << "after substracting z-constraint force from moving molecuels " |
900 |
> |
// << "total force is " << calcTotalForce() << endl; |
901 |
|
|
902 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
902 |
> |
} |
903 |
|
|
904 |
< |
if (states[i] == zcsFixed){ |
905 |
< |
|
906 |
< |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
907 |
< |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
904 |
> |
/** |
905 |
> |
* |
906 |
> |
* |
907 |
> |
*/ |
908 |
> |
|
909 |
> |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
910 |
> |
double force[3]; |
911 |
> |
double harmonicU; |
912 |
> |
double harmonicF; |
913 |
> |
double COM[3]; |
914 |
> |
double diff; |
915 |
> |
double totalFZ_local; |
916 |
> |
double totalFZ; |
917 |
> |
|
918 |
> |
force[0] = 0; |
919 |
> |
force[1] = 0; |
920 |
> |
force[2] = 0; |
921 |
> |
|
922 |
> |
totalFZ_local = 0; |
923 |
> |
|
924 |
> |
for(int i = 0; i < zconsMols.size(); i++) { |
925 |
> |
|
926 |
> |
if (states[i] == zcsMoving){ |
927 |
> |
zconsMols[i]->getCOM(COM); |
928 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
929 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
930 |
> |
|
931 |
> |
diff = COM[whichDirection] -zPos[i]; |
932 |
|
|
933 |
< |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
934 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
935 |
< |
zconsAtoms[j]->addFrc(force); |
936 |
< |
} |
937 |
< |
|
933 |
> |
harmonicU = 0.5 * kz[i] * diff * diff; |
934 |
> |
info->lrPot += harmonicU; |
935 |
> |
|
936 |
> |
harmonicF = - kz[i] * diff; |
937 |
> |
totalFZ_local += harmonicF; |
938 |
> |
|
939 |
> |
//adjust force |
940 |
> |
|
941 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
942 |
> |
|
943 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
944 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
945 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
946 |
> |
movingZAtoms[j]->addFrc(force); |
947 |
> |
} |
948 |
|
} |
712 |
– |
|
713 |
– |
} |
949 |
|
|
950 |
+ |
} |
951 |
+ |
|
952 |
+ |
#ifndef IS_MPI |
953 |
+ |
totalFZ = totalFZ_local; |
954 |
+ |
#else |
955 |
+ |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
956 |
+ |
#endif |
957 |
+ |
|
958 |
+ |
force[0]= 0; |
959 |
+ |
force[1]= 0; |
960 |
+ |
force[2]= 0; |
961 |
+ |
|
962 |
+ |
//modify the forces of unconstrained molecules |
963 |
+ |
for(int i = 0; i < unconsMols.size(); i++){ |
964 |
+ |
|
965 |
+ |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
966 |
+ |
|
967 |
+ |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
968 |
+ |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
969 |
+ |
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
970 |
+ |
unconsAtoms[j]->addFrc(force); |
971 |
+ |
} |
972 |
+ |
} |
973 |
+ |
|
974 |
|
} |
975 |
|
|
976 |
+ |
/** |
977 |
+ |
* |
978 |
+ |
*/ |
979 |
+ |
|
980 |
|
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
981 |
|
double COM[3]; |
982 |
|
double diff; |
983 |
|
|
984 |
< |
bool changed; |
984 |
> |
int changed_local; |
985 |
> |
int changed; |
986 |
|
|
987 |
< |
changed = false; |
987 |
> |
changed_local = 0; |
988 |
|
|
989 |
|
for(int i =0; i < zconsMols.size(); i++){ |
990 |
|
|
992 |
|
diff = fabs(COM[whichDirection] - zPos[i]); |
993 |
|
if ( diff <= zconsTol && states[i] == zcsMoving){ |
994 |
|
states[i] = zcsFixed; |
995 |
< |
changed = true; |
995 |
> |
changed_local = 1; |
996 |
|
} |
997 |
|
else if ( diff > zconsTol && states[i] == zcsFixed){ |
998 |
|
states[i] = zcsMoving; |
999 |
< |
changed = true; |
999 |
> |
changed_local = 1; |
1000 |
|
} |
1001 |
|
|
1002 |
|
} |
1003 |
|
|
1004 |
< |
return changed; |
1004 |
> |
#ifndef IS_MPI |
1005 |
> |
changed =changed_local; |
1006 |
> |
#else |
1007 |
> |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1008 |
> |
#endif |
1009 |
> |
|
1010 |
> |
return (changed > 0); |
1011 |
> |
|
1012 |
|
} |
1013 |
|
|
1014 |
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1015 |
+ |
|
1016 |
+ |
int havingFixed_local; |
1017 |
+ |
int havingFixed; |
1018 |
+ |
|
1019 |
+ |
havingFixed_local = 0; |
1020 |
+ |
|
1021 |
|
for(int i = 0; i < zconsMols.size(); i++) |
1022 |
< |
if (states[i] == zcsFixed) |
1023 |
< |
return true; |
1022 |
> |
if (states[i] == zcsFixed){ |
1023 |
> |
havingFixed_local = 1; |
1024 |
> |
break; |
1025 |
> |
} |
1026 |
|
|
1027 |
< |
return false; |
1027 |
> |
#ifndef IS_MPI |
1028 |
> |
havingFixed = havingFixed_local; |
1029 |
> |
#else |
1030 |
> |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1031 |
> |
#endif |
1032 |
> |
|
1033 |
> |
return (havingFixed > 0); |
1034 |
|
} |
1035 |
|
|
1036 |
|
|
1038 |
|
* |
1039 |
|
*/ |
1040 |
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1041 |
+ |
|
1042 |
+ |
int havingMoving_local; |
1043 |
+ |
int havingMoving; |
1044 |
+ |
|
1045 |
+ |
havingMoving_local = 0; |
1046 |
+ |
|
1047 |
|
for(int i = 0; i < zconsMols.size(); i++) |
1048 |
< |
if (states[i] == zcsMoving) |
1049 |
< |
return true; |
1048 |
> |
if (states[i] == zcsMoving){ |
1049 |
> |
havingMoving_local = 1; |
1050 |
> |
break; |
1051 |
> |
} |
1052 |
|
|
1053 |
< |
return false; |
1053 |
> |
#ifndef IS_MPI |
1054 |
> |
havingMoving = havingMoving_local; |
1055 |
> |
#else |
1056 |
> |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1057 |
> |
#endif |
1058 |
> |
|
1059 |
> |
return (havingMoving > 0); |
1060 |
|
|
1061 |
|
} |
1062 |
|
|
1063 |
|
/** |
1064 |
< |
* |
1065 |
< |
* |
767 |
< |
*/ |
1064 |
> |
* |
1065 |
> |
*/ |
1066 |
|
|
1067 |
< |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
1068 |
< |
double force[3]; |
1069 |
< |
double harmonicU; |
1070 |
< |
double COM[3]; |
1071 |
< |
double diff; |
1072 |
< |
|
1073 |
< |
force[0] = 0; |
1074 |
< |
force[1] = 0; |
1075 |
< |
force[2] = 0; |
1067 |
> |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1068 |
> |
{ |
1069 |
> |
double MVzOfMovingMols_local; |
1070 |
> |
double MVzOfMovingMols; |
1071 |
> |
double totalMassOfMovingZMols_local; |
1072 |
> |
double totalMassOfMovingZMols; |
1073 |
> |
double COMvel[3]; |
1074 |
> |
|
1075 |
> |
MVzOfMovingMols_local = 0; |
1076 |
> |
totalMassOfMovingZMols_local = 0; |
1077 |
|
|
1078 |
< |
cout << "Moving Molecules" << endl; |
1079 |
< |
for(int i = 0; i < zconsMols.size(); i++) { |
1078 |
> |
for(int i =0; i < unconsMols.size(); i++){ |
1079 |
> |
unconsMols[i]->getCOMvel(COMvel); |
1080 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1081 |
> |
} |
1082 |
|
|
1083 |
+ |
for(int i = 0; i < zconsMols.size(); i++){ |
1084 |
+ |
|
1085 |
|
if (states[i] == zcsMoving){ |
1086 |
< |
zconsMols[i]->getCOM(COM): |
1087 |
< |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
1088 |
< |
|
1089 |
< |
diff = COM[whichDirection] -zPos[i]; |
1090 |
< |
|
1091 |
< |
harmonicU = 0.5 * kz[i] * diff * diff; |
789 |
< |
info->ltPot += harmonicU; |
1086 |
> |
zconsMols[i]->getCOMvel(COMvel); |
1087 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1088 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1089 |
> |
} |
1090 |
> |
|
1091 |
> |
} |
1092 |
|
|
1093 |
< |
force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
1094 |
< |
|
1095 |
< |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
1093 |
> |
#ifndef IS_MPI |
1094 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
1095 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1096 |
> |
#else |
1097 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1098 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1099 |
> |
#endif |
1100 |
|
|
1101 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
1102 |
< |
movingZAtoms[j]->addFrc(force); |
797 |
< |
} |
1101 |
> |
double vzOfMovingMols; |
1102 |
> |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1103 |
|
|
1104 |
+ |
return vzOfMovingMols; |
1105 |
+ |
} |
1106 |
+ |
|
1107 |
+ |
/** |
1108 |
+ |
* |
1109 |
+ |
*/ |
1110 |
+ |
|
1111 |
+ |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1112 |
+ |
{ |
1113 |
+ |
double COMvel[3]; |
1114 |
+ |
double tempMVz_local; |
1115 |
+ |
double tempMVz; |
1116 |
+ |
double massOfZCons_local; |
1117 |
+ |
double massOfZCons; |
1118 |
+ |
|
1119 |
+ |
|
1120 |
+ |
tempMVz_local = 0; |
1121 |
+ |
|
1122 |
+ |
for(int i =0 ; i < nMols; i++){ |
1123 |
+ |
molecules[i].getCOMvel(COMvel); |
1124 |
+ |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1125 |
|
} |
1126 |
|
|
1127 |
+ |
massOfZCons_local = 0; |
1128 |
+ |
|
1129 |
+ |
for(int i = 0; i < massOfZConsMols.size(); i++){ |
1130 |
+ |
massOfZCons_local += massOfZConsMols[i]; |
1131 |
+ |
} |
1132 |
+ |
#ifndef IS_MPI |
1133 |
+ |
massOfZCons = massOfZCons_local; |
1134 |
+ |
tempMVz = tempMVz_local; |
1135 |
+ |
#else |
1136 |
+ |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1137 |
+ |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1138 |
+ |
#endif |
1139 |
+ |
|
1140 |
+ |
return tempMVz /(totalMassOfUncons + massOfZCons); |
1141 |
|
} |
1142 |
+ |
|
1143 |
+ |
/** |
1144 |
+ |
* |
1145 |
+ |
*/ |
1146 |
+ |
|
1147 |
+ |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1148 |
+ |
|
1149 |
+ |
double force[3]; |
1150 |
+ |
double totalForce_local; |
1151 |
+ |
double totalForce; |
1152 |
+ |
|
1153 |
+ |
totalForce_local = 0; |
1154 |
+ |
|
1155 |
+ |
for(int i = 0; i < nAtoms; i++){ |
1156 |
+ |
atoms[i]->getFrc(force); |
1157 |
+ |
totalForce_local += force[whichDirection]; |
1158 |
+ |
} |
1159 |
+ |
|
1160 |
+ |
#ifndef IS_MPI |
1161 |
+ |
totalForce = totalForce_local; |
1162 |
+ |
#else |
1163 |
+ |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1164 |
+ |
#endif |
1165 |
+ |
|
1166 |
+ |
return totalForce; |
1167 |
+ |
|
1168 |
+ |
} |
1169 |
+ |
|
1170 |
+ |
/** |
1171 |
+ |
* |
1172 |
+ |
*/ |
1173 |
+ |
|
1174 |
+ |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1175 |
+ |
//calculate the number of atoms of moving z-constrained molecules |
1176 |
+ |
int nMovingZAtoms_local; |
1177 |
+ |
int nMovingZAtoms; |
1178 |
+ |
|
1179 |
+ |
nMovingZAtoms_local = 0; |
1180 |
+ |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1181 |
+ |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1182 |
+ |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1183 |
+ |
|
1184 |
+ |
#ifdef IS_MPI |
1185 |
+ |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1186 |
+ |
#else |
1187 |
+ |
nMovingZAtoms = nMovingZAtoms_local; |
1188 |
+ |
#endif |
1189 |
+ |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1190 |
+ |
|
1191 |
+ |
#ifdef IS_MPI |
1192 |
+ |
if(worldRank == 0){ |
1193 |
+ |
#endif |
1194 |
+ |
// std::cerr << "\n" |
1195 |
+ |
// << "*******************************************\n" |
1196 |
+ |
// << " fiished Policy by numbr()\n" |
1197 |
+ |
// << "*******************************************\n" |
1198 |
+ |
// << "\n"; |
1199 |
+ |
#ifdef IS_MPI |
1200 |
+ |
} |
1201 |
+ |
#endif |
1202 |
+ |
} |
1203 |
+ |
|
1204 |
+ |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1205 |
+ |
return totalForce / mol->getNAtoms(); |
1206 |
+ |
} |
1207 |
+ |
|
1208 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1209 |
+ |
return totalForce / totNumOfMovingAtoms; |
1210 |
+ |
} |
1211 |
+ |
|
1212 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1213 |
+ |
return totalForce / mol->getNAtoms(); |
1214 |
+ |
} |
1215 |
+ |
|
1216 |
+ |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1217 |
+ |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1218 |
+ |
} |
1219 |
+ |
|
1220 |
+ |
/** |
1221 |
+ |
* |
1222 |
+ |
*/ |
1223 |
+ |
|
1224 |
+ |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1225 |
+ |
//calculate the number of atoms of moving z-constrained molecules |
1226 |
+ |
double massOfMovingZAtoms_local; |
1227 |
+ |
double massOfMovingZAtoms; |
1228 |
+ |
|
1229 |
+ |
massOfMovingZAtoms_local = 0; |
1230 |
+ |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1231 |
+ |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1232 |
+ |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1233 |
+ |
|
1234 |
+ |
#ifdef IS_MPI |
1235 |
+ |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1236 |
+ |
#else |
1237 |
+ |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1238 |
+ |
#endif |
1239 |
+ |
totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1240 |
+ |
} |
1241 |
+ |
|
1242 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1243 |
+ |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1244 |
+ |
} |
1245 |
+ |
|
1246 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1247 |
+ |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1248 |
+ |
} |
1249 |
+ |
|
1250 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1251 |
+ |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1252 |
+ |
} |
1253 |
+ |
|
1254 |
+ |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1255 |
+ |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1256 |
+ |
} |
1257 |
+ |
|